Sodium in PDB 7po6: Xist (M6A)Ucg Tetraloop Rna Bound to the Yth Domain of YTHDC1

The structure of Xist (M6A)Ucg Tetraloop Rna Bound to the Yth Domain of YTHDC1, PDB code: 7po6 was solved by A.N.Jones, A.Mourao, M.Sattler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.34 / 1.77
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	78.438, 85.119, 88.617, 90, 90, 90
R / Rfree (%)	20 / 23.2

The binding sites of Sodium atom in the Xist (M6A)Ucg Tetraloop Rna Bound to the Yth Domain of YTHDC1 (pdb code 7po6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Xist (M6A)Ucg Tetraloop Rna Bound to the Yth Domain of YTHDC1, PDB code: 7po6:

Sodium binding site 1 out of 1 in the Xist (M6A)Ucg Tetraloop Rna Bound to the Yth Domain of YTHDC1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Xist (M6A)Ucg Tetraloop Rna Bound to the Yth Domain of YTHDC1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na605 b:78.9 occ:1.00 OE1 C:GLU384 2.5 62.8 1.0 O C:HOH733 2.7 72.2 1.0 O C:MET438 2.8 69.9 1.0 O C:THR379 2.9 58.2 1.0 HA3 C:GLY440 3.0 94.2 1.0 O C:LEU439 3.1 80.8 1.0 HA C:PRO381 3.3 68.3 1.0 C C:LEU439 3.3 75.8 1.0 HG3 C:PRO381 3.3 74.3 1.0 H C:GLY441 3.4 87.7 1.0 HB2 C:GLU384 3.4 65.0 1.0 HA C:LEU439 3.5 79.8 1.0 CD C:GLU384 3.5 70.9 1.0 HA C:LEU380 3.5 68.5 1.0 C C:MET438 3.6 69.7 1.0 O C:HOH711 3.7 56.5 1.0 N C:GLY440 3.7 73.1 1.0 CA C:GLY440 3.8 78.5 1.0 CA C:LEU439 3.8 66.5 1.0 C C:LEU380 3.8 57.1 1.0 HD3 C:PRO381 3.8 69.2 1.0 N C:PRO381 3.8 58.1 1.0 CA C:PRO381 4.0 57.0 1.0 C C:THR379 4.0 55.7 1.0 HB3 C:GLU384 4.0 65.0 1.0 CG C:PRO381 4.1 61.9 1.0 CB C:GLU384 4.1 54.2 1.0 N C:GLY441 4.1 73.1 1.0 CA C:LEU380 4.1 57.1 1.0 CD C:PRO381 4.1 57.7 1.0 N C:LEU439 4.2 63.5 1.0 O C:LEU380 4.2 55.5 1.0 CG C:GLU384 4.3 57.2 1.0 OE2 C:GLU384 4.3 70.3 1.0 H C:GLY440 4.4 87.8 1.0 C C:GLY440 4.4 73.3 1.0 HG3 C:GLU384 4.5 68.6 1.0 CB C:PRO381 4.5 64.2 1.0 HA2 C:GLY440 4.5 94.2 1.0 O C:LYS437 4.6 71.3 1.0 HB3 C:PRO381 4.6 77.0 1.0 N C:LEU380 4.6 54.5 1.0 HA C:MET438 4.6 86.1 1.0 H C:THR379 4.6 66.2 1.0 HE2 C:HIS421 4.7 103.2 1.0 CA C:MET438 4.8 71.8 1.0 HD23 C:LEU380 4.8 75.4 1.0 HG2 C:PRO381 4.9 74.3 1.0 H C:LEU439 5.0 76.2 1.0

A.N.Jones, E.Tikhaia, A.Mourao, M.Sattler. Structural Effects of M6A Modification of the Xist A-Repeat Aucg Tetraloop and Its Recognition By YTHDC1. Nucleic Acids Res. V. 50 2350 2022.
ISSN: ESSN 1362-4962
PubMed: 35166835
DOI: 10.1093/NAR/GKAC080